Unless the OP was unclear, I got the impression that MVC/LA was offered through the HS, not at the CC. In any event, while yes, MVC/LA is a “stronger” option than AP Stats, there are valid reasons for not taking it, like scheduling issues.
I don’t think that one versus the other is a deal-breaker for college admissions, though, unless it impacts the GC’s rigor rating. But as others have said, college credit issues aside, the kid may end up having to take both in college anyway, depending on the college he attends.